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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id$
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 7,
-requires_module => 'IO::String');
use_ok('Bio::Root::IO');
use_ok('Bio::Tools::Run::Phylo::SLR');
use_ok('Bio::AlignIO');
use_ok('Bio::TreeIO');
}
ok my $slr = Bio::Tools::Run::Phylo::SLR->new();
SKIP: {
test_skip(-requires_executable => $slr,
-tests => 2);
# first set
my $alignio1 = Bio::AlignIO->new
(-format => 'fasta',
-file => test_input_file('219877.cdna.fasta'));
my $treeio1 = Bio::TreeIO->new
(-format => 'newick',
-file => test_input_file('219877.tree'));
my $aln1 = $alignio1->next_aln;
my $tree1 = $treeio1->next_tree;
$slr->alignment($aln1);
$slr->tree($tree1);
my ($rc,$results1) = $slr->run();
ok defined($results1);
# second set
$slr = Bio::Tools::Run::Phylo::SLR->new();
my $alignio2 = Bio::AlignIO->new
(-format => 'fasta',
-file => test_input_file('277523.cdna.fasta'));
my $treeio2 = Bio::TreeIO->new
(-format => 'newick',
-file => test_input_file('277523.tree'));
my $aln2 = $alignio2->next_aln;
my $tree2 = $treeio2->next_tree;
$slr->alignment($aln2);
$slr->tree($tree2);
my($rc2,$results2) = $slr->run();
ok defined($results2);
# my $positive_sites = $results2->{'constant'};
# print "Site,Omega\n";
# foreach my $site (@{$positive_sites}) {
# # print "# Site Neutral Optimal Omega lower upper LRT_Stat Pval Adj.Pval Result Note\n";
# print $site->[0], ",", $site->[3], "\n";
# }
# # third set
# $slr = Bio::Tools::Run::Phylo::SLR->new();
# my $alignio3 = Bio::AlignIO->new
# (-format => 'fasta',
# -file => 't/data/799906.cdna.fasta');
# my $treeio3 = Bio::TreeIO->new
# (-format => 'newick',
# -file => 't/data/799906.tree');
# my $aln3 = $alignio3->next_aln;
# my $tree3 = $treeio3->next_tree;
# $slr->alignment($aln3);
# $slr->tree($tree3);
# my ($rc,$results3) = $slr->run();
# my $sites = $results3->{'constant'};
# ok defined($results3);
# print "Site,Omega\n";
# foreach my $site (@{$sites}) {
# # print "# Site Neutral Optimal Omega lower upper LRT_Stat Pval Adj.Pval Result Note\n";
# print $site->[0], ",", $site->[3], "\n";
# }
}
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